Updates

Model and report changes

  1. The model now accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
  2. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
  3. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop .
  4. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
  5. Using observations of improved survival in hospitalised COVID-19 patients, we have allowed the probability of dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) to gradually change over the course of June 2020, with a decrease being estimated. More recently, the Kent variant of the virus has gradually become the predominant virus strain and we accordingly allow for a change in the IFR over the period in which the relative prevalence of this strain has been growing.
  6. The ‘Epidemic summary’ now only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme.

Updated findings

  1. The current estimate of the daily number of new infections occurring each day across England is 5,350 (3,920–-7,160, 95% credible interval). Though infection incidence is currently estimated to be increasing, this represents a small upward revision of our most recent estimate.
  2. The daily infection rate is estimated to be the highest in the North East (NE) with 619 new daily infections, corresponding to 23 per 100,000 population per day. The South West (SW) is the second highest with 797 infections (14 per 100,000). All other regions have 10 new infections per 100k population or less, with incidence in the North West appearing to be particularly low (2 infections per 100,000). Note that currently these regional estimates are particularly uncertain and that a substantial proportion of these daily infections will be asymptomatic.
  3. We predict that the number of deaths occurring daily is likely to remain low but also likely to start increasing. For the 11h June we forecast between 25 and 67 daily deaths.
  4. The probability of Rt exceeding 1 is 84% and 83% in the NE and SW respectively; around 60% in the East of England (EE) and both East and West Midlands (EM & WM); 30–40% in the London (GL), South East (SE) and Yorkshire and Humber (YH) regions; and 5% in the NW.
  5. The growth rate for England remains at 0.01 (0.00-–0.02, 95% credible interval) per day. This means that, nationally, the number of infections is likely to be increasing, although there is considerable uncertainty and heterogeneity across regions, with negative growth in many, the NW in particular.
  6. London, followed by the NE and the WM, has the highest attack rates, that is the proportions of the regional populations who have ever been infected, with 27%, 23% and 22% respectively. The SW continues to have the lowest attack rate at 12%. The attack rate in London constitutes a 5% downward revision from our previous published report.
  7. Note that the deaths data used are only very weakly informative on Rt over the last two weeks and are thankfully becoming increasingly sparse. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of the estimated Rt in the most recent weeks show reasonably stable values despite the gradual relaxation of pandemic mitigation measures. Going forward, an increase is anticipated in the coming days, a consequence of the ongoing relaxation of restrictions, before a transient drop over the school half-term week. The Rt for five regions have central estimates just above 1 (EE, EM, NE, , SW, WM), although these estimates are uncertain. At current levels of incidence, these values of Rt are not a particular concern, though they do require careful monitoring.

The incidence of deaths has continued to fall more sharply than predicted by the model, which predicts that there will be a gradual rise over the coming few weeks.

The plot of the infection fatality rate (IFR) presents age-specific probabilities of death given infection. It shows an increasing mortality risk from September onwards in all ages until the immunisation programme begins to have an impact in late January. From the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop measures the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 7% in the over-75s and 0.3% overall. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people; older age groups are immunised and become protected against infection. The impact of the second immunisation doses (initially in the 45-64) becoming widespread will begin to affect this quantity over the coming weeks.

Estimates of cumulative infection are low in comparison to some earlier reports. This is due to the inclusion of the prevalence data, which appear to have the effect of reducing the number of infections. Nowhere is this more true than in the North West, where estimates of attack rate have fallen to 18%. London remains the region with the largest levels of cumulative infection to date. Other indicators (e.g. hospital bed prevalence, reported new cases) are now beginning to suggest a resurgent epidemic, largely due to the increasing presence of the B.1.617 strain. Prevalence of infection, as estimated by the ONS Community Infections Survey is under 0.10% in England with some regional heterogeneity. Given the low prevalence, the increasing transmission is not an immediate concern, but the presence of a rapidly spreading new strain does provide some alarm. We will continue to monitor the situation closely.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.
  3. Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

Current IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.01 0.00 0.02
East of England 0.00 -0.02 0.03
East Midlands 0.00 -0.04 0.03
London -0.01 -0.04 0.02
North East 0.01 -0.01 0.04
North West -0.03 -0.05 0.01
South East 0.00 -0.03 0.03
South West 0.02 -0.02 0.04
West Midlands 0.01 -0.03 0.03
Yorkshire and The Humber -0.01 -0.04 0.02

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 187.07 NA
East of England NA 33.23 NA
East Midlands NA 19.42 NA
London 116.04 18.78 NA
North East NA 51.35 NA
North West 26.29 13.08 NA
South East 150.16 21.08 NA
South West NA 41.70 NA
West Midlands NA 20.92 NA
Yorkshire and The Humber 105.00 17.55 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 83.62 34.42 NA
East of England 163.28 25.09 NA
East Midlands 322.01 20.64 NA
London NA 35.22 NA
North East 55.54 17.72 NA
North West NA 134.99 NA
South East NA 26.93 NA
South West 45.41 15.60 NA
West Midlands 126.80 20.69 NA
Yorkshire and The Humber NA 30.16 NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.00 -0.01 0.01
East of England 0.00 -0.02 0.02
East Midlands -0.01 -0.04 0.02
London -0.01 -0.03 0.02
North East 0.01 -0.01 0.04
North West -0.03 -0.05 0.00
South East -0.01 -0.03 0.02
South West 0.01 -0.02 0.04
West Midlands 0.00 -0.03 0.03
Yorkshire and The Humber -0.01 -0.03 0.02

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 472.12 63.48 NA
East of England NA 30.68 NA
East Midlands 87.12 18.79 NA
London 70.35 23.53 NA
North East NA 45.98 NA
North West 25.80 15.01 1374.01
South East 109.02 24.61 NA
South West NA 41.90 NA
West Midlands 375.76 21.28 NA
Yorkshire and The Humber 74.45 20.93 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 86.25 NA
East of England 3012.02 28.41 NA
East Midlands NA 29.95 NA
London NA 41.22 NA
North East 70.49 19.26 NA
North West NA NA NA
South East NA 35.40 NA
South West 65.96 17.09 NA
West Midlands NA 25.61 NA
Yorkshire and The Humber NA 39.10 NA

Infections and deaths

The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (21 May).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

IFR

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

Copyright © MRC Biostatistics Unit, University of Cambridge